10 Years One Day
by wiccafaith
Summary: Series: AU as of S1: The Wraith were too much of a threat to Atlantis to risk going home. But now they have been defeated Rodney and John have to face far more difficult obsticles. SLASH McShep - please read 'First Kiss' for background vignette. R&R.
1. Prologue: One Way Trip

Fandom: Stargate Atlantis

Title: 10 Years and One Day (2014)

Pairings: Rodney McKay/John Sheppard, Elizabeth Weir/OMC, Ronan Dex/OFC, Teyla Emmagen/Kanaan, Vala/Daniel Jackson.

Characters: Rodney, John, Elizabeth, Ronan, Teyla, Sam Carter, Daniel Jackson, Vala… many OCs.

Genres: Slash, AU

Plot summary: In 2004 the Atlantis expedition began. A few weeks after their first encounter with the wraith and Elizabeth gives them a choice. They choose not to risk Earth while the Wraith are still a threat. Ten years later they are free to go home; but what if Atlantis is their home now and what if everything has changed in ten years?

**PROLOGUE: ONE WAY TRIP**

"Ready?" Dr Elizabeth Weir asked as she stood next to the comm. link in her office that would enable her to talk to every Atlantis resident simultaneously. Outwardly she appeared calm and in control but inside worry and fear was gnawing at her. Yes, they had always knew it could very well be a one way trip; after all there had been no guarantee that Atlantis would have enough power to dial up Earth just as they knew Earth wouldn't be able to re-dial Atlantis without a lot of extra power. But knowing it going in and facing the opportunity to go home or at the very least have contact with home was all together something completely different.

McKay – visibly nervous and jumpy, one hand holding an energy bar and the other tapping his PDA absently – nodded, clearly eager to get this over with. John, stood next to Rodney, was still but she could clearly read the trepidation in his eyes as clearly as if she had known him their whole lives.

"Lets do this then," she agreed and pressed the switch to initiate city-wide comm. systems. "Atlantis, this is Dr Weir talking. I know that some of you have hear a rumour that we have a method to communicate with – or maybe even take us back to Earth. This is true to a certain extent. Dr McKay has devised a way to establish contact with Earth. However our military leader believes this may be dangerous. As we have already experienced, the Wraith are a formidable enemy and the fact they feed off of humans means that Earth would be an ideal feeding ground for them. I believe that this decision is not mine alone but that all Atlantis personnel should get a vote. We all knew this could be a one way trip but now I am telling you there is a chance to go home – see your loved ones and walk on the Earth again. It is up to all of us to chose to go or stay. If the majority vote is to stay then we will focus all our attention to defeating the Wraith so that one day we may be able to safely dial home again. This vote will be taking place in one weeks time. Thanks you." Elizabeth switched off the system and sunk into her chair. Rodney shared a worried glance at John. "God, I hope we are doing the right thing." Elizabeth muttered.

(One week and one day later)

"Is it done?" Elizabeth asked. The vote had been cast and every Atlantean resident had come forth to vote yes or no on the 'do we or do we not dial home' question. Teyla, John, Rodney, and a few trusted others had been rounded up to count the votes and report back to Elizabeth so she could judge it and inform the base about the results. Truthfully they all looked terrible, Rodney was so stressed about this whole thing he was barely even eating, Teyla was dealing with the worries of her own people who had taken refuge on the mainland, and Elizabeth hadn't been able to sleep all week.

John nodded. "Every vote accounted for. Triple checked." He confirmed with a nod.

"And?" Elizabeth asked, her voice sharp with tension.

"Your people have voted to stay in the Pegasus galaxy until the Wraith are no longer a threat to Earth, or the peoples of this galaxy." Teyla revealed smoothly, her voice radiating calm and peace as Elizabeth absorbed the news.

"What were the percentages?" She needed to know how many people she was denying in order to deal with the fall out. Rodney, Teyla, and John once again exchanged meaningful looks.

"Well… I… there…. It's a hundred percent. Everyone wants to stay." Rodney finally spat out.

"My god. I never expected…" Elizabeth was speechless.

"The level of self-sacrifice your people have shown is a testament to how much you all wish to protect your loves ones. You are a very brave people, Dr Weir. Welcome to the Pegasus galaxy." Teyla said formerly.

"Home sweet home," Elizabeth whispered, staring at the photograph of her and her mother on the desk. She would probably never see her mom again, but at least she knew that her mom would be safe from the Wraith. They were doing an honourable thing. And Elizabeth hoped that was enough to help them all sleep at night.

That night Elizabeth dialled Earth for the first and possibly lat time. They had recorded a one way message for Earth, most of them had left small personal messages but Elizabeth had added a message for Stargate command. It went like this;

_This is Dr Elizabeth Weir of the Atlantis base of command in the Pegasus galaxy. It is important that you know we arrived safely at our destination and everyday this city is teaching us new things to aid us. But we have encountered an enemy possibly even worse than the Goa'uld or the Replicators. They are called Wraith and they feed on humans. It is the vote of this base that we do not contact Earth again until the Wraith are defeated. This may not be a goal we can achieve in my lifetime but it is something we will work towards until the day we can return home. Do not attempt to reconnect with us or send any messages from Earth. We can't risk them discovering you. Goodbye."_


	2. Chapter 1: Victory

**CHAPTER ONE: VICTORY**

John lies in bed, his head resting on Rodney's bare stomach as McKay reads some sort of computerized report from one of his many minions in the science department that he heads up on Atlantis. John's mind is quiet and relaxed in post-coital bliss, the familiar smell of sex and Rodney filling the air as he lounges their as if he had not a care in the galaxy. But at the back if his mind a darkness is gnawing at his serenity. Yesterday they had celebrated their victory in wiping out the Wraith. Those who were not dead and rotting were successfully humanized enough that they no longer possessed the ability to drain life from humans and now ate regular mortal food. While it shortened their lifespan considerably it was serving its purpose by improving the quality and length of everyone else's life in the Pegasus galaxy. Treaties were in place with Wraith-human hybrids such as Todd, and Elizabeth had decreed that they would dial home in the morning. The base was alive with apprehension and excitement. John couldn't help but think that his feelings were more negative than positive. After all Earth meant military regulations like obeying people with more authority than him – which was fair few people since technically his rank was only that of a Major as no one here had the authority to change it officially – and 'don't ask, don't tell' and fraternisation regs. Basically, rules that he would be expected to follow that would keep him away from Rodney. And John knew that after ten years he couldn't do that. No matter the cost.

"Stop worrying. That's my job." Rodney demanded.

"I'm not worrying. I'm thinking." John corrected.

"Huh, well that's also my job. You can just lie there and look pretty." Rodney told him, giving him a condescending pat on his head.

John sent him a half hearted glare. "Or I could go get my gun and shoot things. After all, that's my job right?" He suggested.

"No, no, that's okay." Rodney gulped. "But seriously John, stop worrying. It'll make you go gray and then I'll have to be the pretty one and we both know that'll never work… what are you worrying about? You should be excited. We get to go home tomorrow." Rodney babbled, sounding pretty unexcited and worried himself.

John shifted so he could look into his partner's eyes. "You still think of Earth as home?" He asked, frowning.

"No… no it's just…. You have a brother and an ex-wife and old Air Force buddies… why? Don't you think of Earth as home?" Rodney asked, his blue eyes shining with his own fears and insecurities.

"No," John denied. "Atlantis is my home, it has been for more than nine years now. And you're my home too. Of course I miss people back on Earth but I can live without them. Honestly I'm not sure I could live without you." He admitted.

Rodney beamed a smile of honest happiness and relief. "Thank god because I feel the same way!" He declared.

"That's because you love me." John smiled smugly.

"Or because I'm so used to having you around that I'm not sure what to do when you're not here." Rodney joked lightly.

"Either way I get sex." John pointed out snuggling up to his lover. He was planning to sleep but truthfully, as soon as he closed his eyes the darkness seemed to overwhelm him, taunting him with is own fears that going back to Earth would be the worst thing for all. He was so scared.

"Sssh." Rodney whispered comfortingly. "Just listen to my heartbeat." He told him and John pressed his head against Rodney's chest focusing on the comforting thumpa-thumpa of his lover's heart, soothing and reassuring.

"Why am I panicking and you're so calm?" John asked. Usually it was the other way around.

"You think I'm calm? You should have seen me earlier. I kept dropping things and stuttering. My heart was going like the celebration drums on Harvest night on P4-XX552L. I thought I was going to have a heart attack and the Doc had to prescribe some pills to calm me down. But honestly I feel better knowing you're panicking." Rodney admitted.

"Hey!" John whined, not liking the sound of that.

"No, not in a mean way. It's just… if you're panicking it means you're afraid of losing me, of losing this. And that means you really do love me." Rodney said, sounding very self-conscious.

"Of course I love you. I have for more many years and that's not going to stop just because I'm back on Earth." John told him.

"Good. I love you too. Now can we go to sleep now?" Rodney asked and John rolled his eyes, nodding in agreement. Despite this, neither slept that night. They just lay there listening to the sound of their hearts beating and the waves beating against the city exterior. The sounds of home.


	3. Chapter 2: Contact

Guys; maybe this is the wrong time of year for this or maybe I'm jumping the gun a bit because its only been up for a day or so but **please review**! This is **my very first SGA fiction ever** and its been an idea I've had for years and always wanted to write. **I will be publishing the first five chapters** regardless as I have already written them but after that I usually rely on readers to help me through the dry spells! Anyway, I know I have one reader so THANKS!

**CHAPTER TWO: CONTACT**

Most of Atlantis was packed in the main gate room as the wormhole to Earth was established. Claps filled the room for a few seconds as they heard the greeting from the SGC on Earth.

"Hello, General Landry. This is Elizabeth Weir speaking from Atlantis." She greeted him.

"Well its about time!" He told her. "Greetings from Earth. How have you been, Dr Weir. I take it this means you finally defeated the Wraith?" He asked.

"Indeed we have, General. What are left of the Wraith we count among our allies having fully disabled their ability to feed on humans. They have no need to come to Earth now and we believe its time to re-establish contact with you." Elizabeth reported.

"Congratulations. I'll inform the IOA and the President as well as United Nations of your success and we'll make plans to bring you home." Landry informed her.

Elizabeth sent a glance behind her at her husband, Kelac, who was a native of the Pegasus galaxy, and then at Teyla with her son in her arms, and John and Rodney who stood side by side determined to make it through this together. She squared her shoulders and turned to face Landry's image. "No offense intended, General, but for most of us; this is home. Of course people are eager o visit family, old friends, but not everyone is interested in taking up a permanent residence on Earth once again. You must understand that much has changed in ten years." Elizabeth said, and John took a breath that he hadn't realised he'd been holding in.

General Landry looked confused for a moment but his professionalism overtook him. "I understand," he said, although it was clear he didn't. "I'll tell the concerned authorities but as you know this is over my head, I can't make any promises." Landry told her. Elizabeth nodded sharply. "You'll dial us again at 1400 hours?"

"Yes. Dr McKay has a method that you can implement at a later date to make a wormhole at your end, but for now we'll call you." She told him. "Talk soon. Over and out." Elizabeth mined a throat-cutting slash to indicate she wanted Amelia to cut communications.

"That went well," John said mildly as Landry's image disappeared and the wormhole disappeared.

"Did it?" Elizabeth said dryly, not so sure herself.

"Well at least he didn't demand we march straight through the gate right this minute." John pointed out.

"Yes but he didn't say we would be able to stay either." Elizabeth worried. Kelac, a large man with dark hair that was starting to go grey and wide expressive green eyes embraced his wife.

"You feared this outcome, Eliz," he reminded her in his gruff Tamaean accent, using the nickname he had always used for her. "That is why you did not give them Dr Rodney's programme for contacting Atlantis. So you wouldn't have to worry about them coming here and ordering you out."

"I know. Doesn't mean they won't try anyway." Elizabeth said and everyone shared concerned glances as they thought about their futures.


	4. Chapter 3: Orders

**CHAPTER THREE: ORDERS**

"Are you ready, Rodney?" John asked, watching as his nervous lover typed madly on the keyboard of one of the Atlantean consoles. John wasn't sure what exactly he was doing – his grip on the language was still fairly basic and despite his almost-Mensa membership he didn't understand the science behind more than half of what Rodney or his team did.

"No," Rodney admitted. "I have a really bad feeling about this. Like Michael-bad."

John didn't like seeing Rodney like this, which was strange as he was often in one kind of panic or other whether fearing for his life due to alien threats or possible citrus-ingestion. This was different. And John couldn't help but think that Rodney's 'Michael-bad' was exactly how John was feeling. "It'll be okay. We'll stick together." John assured him, rubbing his back. "Now come on, it's almost time."

They made their way up to the gate room by using several of the teleporters. Rodney wasn't keen on stairs and there wasn't much time to lose. By the time they arrived Elizabeth had already dialled Earth and there were three familiar faces staring at them from the computer screen.

"Hi, Sam. Daniel. General Landry." Rodney greeted them.

"Rodney," Sam sounded surprised. "It's… good to see you again." Rodney slightly resented the pause before 'good' thinking she had meant 'surprising'. Hadn't she expected him to survive ten years in an alien galaxy?

"I'm surprised to see you too, Carter. Haven't you retired yet?" He asked slightly sarcastically. Sam winced realising she had offended the scientist.

"No. I'm in charge of the Daedelus. General O'Neil semi-retired though, and Teal'c returned to the new Jafar home world. Daniel and Vala are still at the SGC – although in a much more advisory position. SG1 is made of entirely new members, headed by Colonel Mitchell now." Sam told them.

"Who's Vala?" Rodney thought out loud.

"My wife." Daniel admitted.

"Oh. Congratulations." Rodney said.

"Moving on to _other_ matters," Elizabeth said, trying to focus them all. "You were about to tell me of the IOA's decision regarding the Atlantis expedition."

"Right," Landry agreed. "The IOA have decided that Atlantis will stay as an Earth base in the Pegasus galaxy, there is still much that we can learn from the Ancients and what they have left behind. Using Dr McKay's program we can establish a two way gate between our galaxies and exchange information, mission reports, politics, and personnel much easier than any other method that has been considered." They all breathed a sigh of relief, but more was yet to come. "However they wish to review all key personnel's performances as well as replacing some of the staff. Any personnel who wish to return to Earth can do so immediately and will be debriefed extensively before heading out into the real world."

"No offense, General, but I think our defeat of the Wraith threat and our continued existence here speaks for itself as to our performance." Elizabeth said, tightly controlling her anger.

"Maybe so, Doctor, but the fact remains that the IOA have issued these orders and expect to have them followed. Now, yourself, Major Jonathan Sheppard, and Dr Rodney McKay need to be among the first group back to Earth." Landry continued. Sam looked slightly sorry about this but Daniel seemed distracted, possibly by the chance to get his hands on Atlantis finally.

"Of course. We will be arriving shortly. Is that all?" Elizabeth asked, her nails digging into the palms of her hands. Never hand anything upset her so much as the possibility of losing her home. But she knew that to refuse now could be spectacularly disastrous.

"Um, no. I'm going to be coming back. First I'd like to speak to Dr Weir and then I'll be coming through the gate as soon as the programme is written and I'll need someone to show me around and explain things to me." Daniel said, excitement barely contained.

"Of course. I'll have Dr Zelenka and Teyla free to help you." Elizabeth said.

"Okay, that's all. See you at 1800 Dr Weir." Landry nodded before the transmission was terminated.

The silence in the gate room was defining. "Well," Elizabeth said sharply after a long pause. "Better get packing then." She said before storming off, probably to find her husband who had opted out of being here this time.

"Yeah. Us too, I guess." John said, feeling slightly dazed. He left, not looking to see if Rodney was trailing behind or not.

"Rodney?" Teyla approached the still figure of her teammate, she was now baby-less thanks to Kanaan returning from his trip to the mainland and looking after their son. She reached out and placed a hand on his shoulder. "Rodney, are you well?" She asked, concern filling her melodious voice.

Rodney jumped slightly having been in a world of his own. That world was filled with misery and the pain of losing John to his military obligations. "No. I mean yes. I'll be fine. But what about Chitara? And Liron?" He said. Chi and Liron were his and John's 'adopted' children. Liron's village had been culled by the Wraith, and on a mission John had come across the child holed up in one of the Wraith ships waiting to be fed upon. Chitara was a different case, her parents had been Wraith-worshipers who had only born a child in order that she could grow and become a food source for the Wraith. When they had found her upon an infected Wraith ship she had had no language skills and Rodney had basically taught her everything. The children were very attached to their 'foster father's' but spent much of their time on the mainland learning farming and culture from the Athosians.

"I will check in on them and tell them of what is going on. But there is no need to worry yet, surely. It is entirely possible you will be able to return after they have spoken to you, is it not?" Teyla asked.

"Um… possible yes, likely no." Rodney said.

"They will always have people to take care of them, Rodney. You just do your best to come back. Goodbye and good luck." Teyla told him as Rodney finally moved towards the door.

"Goodbye," he whispered almost to himself.

AN// THANKS TO [sparklyshimmer2010] thanks and I hope you enjoy! Thanks so much! I very much appreciate reviews and I hope you have fun exploring SGA/slash!


	5. Chapter 4: Home is Where the Heart Is

**CHAPTER FOUR: HOME IS WHERE THE HEART IS**

"Welcome back." Landry greeted them on the other side of the wormhole. Rodney stared forlornly at the closing gate. The SGC had not changed much, still covered in cold unwelcoming concrete and filled with gunned airmen with stern expressions on their faces. What a welcome, Rodney reflected.

"McKay, you are with Sam. Weir go with Daniel. And me and Sheppard are going to have a little chat." Landry informed them, and walked away before any arguments could be made. John stalked after the General, Weir shrugged and followed Daniel who immediately started asking questions, and Rodney snapped his mouth shut. It seemed no one else was going to fight for the right to return to Atlantis, then why should he. An image of Chitara crying after nightmares and of Liron holding a stick in preparation to learn how to fight, that stubborn angry expression on his young face, filled Rodney's mind and he made himself a vow that even if John didn't manage to get them out of this mess, he would. Yes, yes, he knew how that sounds. Rodney McKay was not your typical hero, in fact he didn't even like children most of the time, but this was different. This wasn't about being a hero, it was about being the person he had tried so hard to become. Besides, even if this wasn't the actions of the old Dr Rodney McKay, it was at least an statement as arrogant as any he had ever made.

"So… welcome home." Sam said as they stood awkwardly in her old office.

"Yeah, 'home'," Rodney said sarcastically.

"Do you have any plans? Anything you want to do while on Earth?" Sam asked, seemingly determined to have a civilised conversation.

"Well I thought I'd maybe visit my sister… but as I haven't spoken to her in…. oh say twelve years I expect to have the door shut in my face so it'll probably be a short visit. Then I hope to leave." Rodney told her in his usual abrupt but honest way.

"You really don't want to be here? At all?" Sam seemed completely confused by the concept.

"Earth isn't my home, Sam. It's just the planet I was born on. In Atlantis I'm happy. I have family, friends, a purpose even if I can't publish anymore." Rodney sounded like the last one was a big issue for him, and that didn't surprise Sam at all.

"I'm glad you have a home, Rodney. And I really do hope you get permission to stay there and for what its worth, I think you will. Lets get to work, the quicker we get this finished the sooner you can go back home," Sam said and then started asking him questions, starting with the condition of Atlantis when they arrived.

**_**

"Major Sheppard, I need you to tell me the events that led to you assuming military command over Atlantis. When you left, the commanding officer was Colonel Sumner, when and why exactly did that change?" Landry asked. John had followed the General to the debriefing room where he was met my an IOA representative and General Jack O'Neil. John stared at the inactive gate wanting nothing more than to dial Atlantis and return to the safety of the Ancient city.

"It changed when he died." John told them insolently. He figured that he wouldn't be surrounded by authority figures if they just wanted a friendly chat. That and the two armed guards near the stairwell told John that he wasn't going back home anytime soon.

The IOA rep sent a glare in John's direction before scribbling down some notes on her thick pile of paper and files. "Which was when, Major?" General O'Neil said with dry bite to his words.

John wished they wouldn't keep saying 'Major' as if reminding him of his own lack of power on Earth and that a Major shouldn't be in control of a whole city. "Sir, Colonel Sumner died during our first encounter with the Wraith ten years ago. Ever since I've been the ranking military officer in Atlantis and Elizabeth has trusted my decisions to protect our people from all kinds of threats, be it the Genii, the Wraith, or the Replicators."

"How was Sumner killed?" the IOA rep asked in her cold voice.

"We were capture – Colonel Sumner, me, Ford, and several of the Athosians. They… beamed us upon a Wraith ship and Sumner was taken to see the Queen. She drained his life force but before she had killed him completely I shot him to put him out of his misery. There was nothing anyone could have done, he was already dead. It's all in my first mission report in the Atlantean computers; I'm not trying to hide anything. Sirs. Ma'am." John said defensively. He knew how it looked. Guy how already ahd a problem with authority is sent to a far away situation only because he has a rare gene, and then that guy's commanding officer just happens to die and the guy takes over? It would look suspicious to John if he weren't the subject of this theory.

"Major, we're going to have to obtain those files quickly, and then we'll be having a long chat," Colonel Landry told him and with a nod the two guards came to stand either side of John. He eyed them warily but didn't put up any fight when they escorted him to a SGC overnight room. At least it wasn't a cell, he reflected as he lay on the bed staring at the concrete ceiling. Of course with no window and a locked door with guards outside, a cell was exactly what it felt like.

*_*

Sam sighed, rubbing her forehead and shutting down her laptop. "So, okay that's all we need for today-"

"Today! It's been like five already!" Rodney exaggerated.

Sam gave him her 'don't be ridiculous' look. "Rodney, it's been thirty hours and you've had breaks."

He looked slightly mollified. Slightly. "Okay, okay. So can I go now? I mean am I cleared to leave the base right?" He asked.

"Yeah of course. Most of the personnel who returned with you already have left the base. You have to be checked out by Dr Lam first but afterwards you can go wherever you want to." She confirmed.

"What about John? And Weir?" Rodney asked, trying not to sound too eager for information about his absent lover. Truthfully this whole being-parted-thing was making him nervous. Even talking about all the technological wonders they had discovered over the last ten years hadn't distracted him from John's absence.

"I believe Weir went home last night and… Rodney, about Sheppard…." Sam began delicately.

"Oh what," Rodney groaned, dread filling his stomach.

"He's being detained until the details surrounding Colonel Sumner are cleared up." Sam continued, wincing at the sheer intensity of the panic and disbelief of Rodney's expression.

"No but that's ridiculous! I mean come on, Sheppard couldn't hurt a fly let alone kill his commanding officer in cold blood! Seriously, don't tell me that Generals O'Neil and Landry are buying this crap!" Rodney wore crudely.

"I'm not sure but I know that the IOA representative is pushing to have John discharged from the Air Force which would cut him off from Atlantis. They are also pushing to have Dr Weir return to Earth and have her replaced by a more… 'suitable' representative. Their word, not mine." Sam explained.

"This is… we didn't have to come back. Hell, I didn't want to. We were perfectly happy back in Atlantis and away from your stupid regulations and politics." Rodney spouted off before grabbing his jacket and storming off, ignoring Sam's attempts to call him back. Fury clouded his mind. How could they detain John after everything he had done for the people of Atlantis and the Pegasus galaxy.

It didn't take long for Rodney to find John. He already knew his way around the SGC from his time here working with Carter before the Pegasus Project had even been thought of. Although this time it was more of a case of 'follow the trail of gossip and armed guards' and woah, at the end of the trail was his pot of gold. John Sheppard. Major John Sheppard. And locking him up like this was more than just wrong.

Rodney approached the door, glaring coldly at the armed guards and flashing the ID card he'd been given. "Let me in," he demanded.

The guards exchanged looks. "No sir, we can't do this. Major Sheppard is being detained until further notice." One of them said as if repeating lines from a script. Rodney barely resisted the urge to roll his eyes.

"Listen, Lieutenant, I am not a security threat. I am an employee of this base just like you," well, not _just like him_, obviously, but Rodney honestly wasn't trying to antagonise the man, "so you are going to unlock that door and let me inside to visit with the Major. Once I am inside you can lock the door again – I don't care. Now, please let me into the Major's room." Rodney folded his arms and straightened his back attempting to look as threatening as possible. But honestly he believed it was the very real and very cold hard glint in his eyes that said he was a man on the edge who would not be taking 'no' for an answer. The two Airmen shared a look and with a nod one of them unlocked the Major's room and allowed him inside.

"Thank you." Rodney said coldly before the door swung shut and the lock turned once again.

"McKay?" John said, sounding out of sorts.

"It's me John." Rodney confirmed. "How are you? They told me…. It doesn't sound good." His worry and fear showed on his expressive face.

John looked at the door nervously. He charged towards Rodney embracing him in an intimate hug and breathing deeply into his neck. "It's okay. As long as we stick together." John repeated, like a mantra, like it was all he had going for him right now.

"That's the problem," Rodney said miserably. "They're trying to separate us."

John stiffened but Rodney was pleased that he didn't back away. "I know," he muttered hoarsely. "I knew it as soon as I entered that room and that IOA bitch was sitting there looking as cool as ice cubes. She's already made her mind up about my involvement with the Pegasus program and lets just say I'm not IOA material." He moved away to sit on the cot.

"But you can still convince the Generals. They've both been in war-like conditions before. They know that sometimes things happen that you neither want or need. I haven't given up hope." McKay told him fiercely.

John nodded almost to himself before lifting his beautiful green eyes to meet Rodney's. "Good. Neither will I then." And Rodney smiled.

===== //=====

I have apparently given up in inspiring people to comment. Oh well. Thank you for those who did! YOU KNOW WHO YOU ARE! I send you a virtual hug!


	6. Chapter 5: Visiting

**CHAPTER FIVE: VISITING**

"How long can you stay?" John asked, running his hands over Rodney's clothed body, his intentions clear.

"Tonight – I want to visit my sister tomorrow but I can come back afterwards." Rodney told him.

John nodded, ignoring the silent 'if they let me' as he pulled Rodney closer and rolled them both on to the waiting cot. "Good," he whispered against his mouth before his lips started sucking at Rodney's, his tongue exploring the mouth he knew so well yet could never get enough of. He didn't even care that that sounded corny.

"Are we seriously going to do this with two armed guards outside?" Rodney interrupted their making out to ask.

"Yes! Besides it's not like it would be the first time." John said, remembering vividly being captured on P5-KS223 and the activities he and Rodney had amused themselves with as the occupants had attempted to blackmail Elizabeth with their lives. They had certainly been inventive considering their arms and legs had been bound.

"Yeah but that wasn't on a US air force secret base!" Rodney said trying to ignore the fact he was blushing.

"It doesn't matter. I'm pretty sure the room is sound proof or something, there isn't a window so they can't see and we'll hear the locks if they go. Besides, I want you." John said, his voice smoky and seductive.

Rodney would deny it later, but at the sound of his lover's voice he melted. "Well, when you put it like that…." John wrapped his arms around Rodney and deepened their previous kisses. That night both men gave into their fear and desperation and kissed like they were never going to see each other again, whispers of 'I love you' and 'never leave me' were mixed in with the unmistakable sounds of moans and grunts. Finally they fell asleep, their bodies satiated but their minds preoccupied. Both men had nightmares that woke them in the early hours, but neither would talk as they lay there in the dark clinging to each other like that alone could save them.

In the morning, or rather late morning, Rodney quietly started to dress. John gazed at him with all his love and pain shining in his eyes, but he knew that Rodney really wanted to see Jeannie so he kept quiet as his lover slipped away. "I'll see you later, okay." Rodney promised, and with one nod from John he walked out the room and away from the man he loved.

Canada – 1500hrs approx.

Knock, knock, knock. Part of Rodney couldn't believe that Jeannie still lived in the same house that she and her husband… Karl? Conrad? Whatever-his-face-was had moved into shortly after they had married thirteen years ago. A house that even though Rodney had only visited once he still remembered like the back of his hand – or rather like Pi to 15 decimals. Maybe it was because he felt so guilty for letting her down, for not being the brother she deserved. Yes, he had only said those things because he wanted her to be happy, but in the long run none of that mattered. He missed her.

"Coming!" A harried voice yelled from inside the house. Rodney would have smiled if he wasn't so nervous, she sounded just the same as always. Still his little sister, no matter what.

The door opened. Stunned silence as the blond haired women surveyed the sight in front of her. "Meredith?" She asked, shocked.

Rodney smiled a polite-but-nervous smile as he handed her a small bouquet of flowers eh had picked up at a gas station on his way over. "Jeannie." He replied. "You look good," he said, not lying.

"You look… old." Jeannie responded. Then, to Rodney's shock, she flung herself at him and hugged him. He stiffened, not sure what to do as they weren't a very demonstrative family. When Jeannie stepped back he could see that tears had formed in her eyes. She tried to blink them a way and sniffed delicately. "Sorry." She apologised. "It's just… it's so good to see you." She gave him a watery smile and let him inside.

"Okay! Who told you I was dead?" Rodney asked, figuring it was the only reason she would be so willing to let by-gones be by-gones and be so happy to see him.

"No one." She frowned at him as she put the flowers in a vase. "I'm just happy to see you, big brother."

"I know. Which was why I asked it. After all the last time we saw each other it didn't exactly end well." He admitted uncomfortably.

"Well yeah, because you were a pig-headed narrow minded idiot." Jeannie informed him and Rodney mentally rolled his eyes, yep; still his sister.

"I'm probably still those things," he warned her.

She shrugged. "I know. But you've been trapped in another galaxy for the past ten years so I figured you may have changed a little."

Rodney let his mouth hang open in a very unattractive manner as he stared at his sister. "You… what… I mean… how…. Huh?"

Jeannie smiled. "I wrote a math proof a few years back. Spur of the moment. It turned out that some of the research the SGC were conducting could use what I wrote. So they let me in on the big secret and when they realised you were my brother they told me about Pegasus and let me see that clip of the video you recorded for me? Thanks, by the way. Anyway, ever since Madison started full time at school I've been freelancing for them from home." She told him.

"That…. That's great, Jeannie." Rodney said.

"How about you Mer, how's the love life?" Jeannie smiled the smile of a sister fully prepared to interrogate her brother and Rodney choke don the glass of water she had handed to him.

"Um… I… I… er…." Rodney stuttered.

"Now this has got to be good!" Jeannie said, her eyes gleaming with the hint of gossip. "Who is she?"

Rodney took a deep breath and reminded himself to be brave. John would want Jeannie to know about them. "Him." He corrected her. "We're married." With this admission he was rewarded with his sister's utterly gobsmacked expression. Victory.

"You got married! To a guy! Jeez, Meredith, I didn't know you had it in you!" Jeannie exclaimed.

Rodney's eyes flashed at the perceived slight; either Jeannie didn't believe he could be gay or she didn't believe he could commit enough to get married. Still, he was trying to mend bridges here not burn them and ten years stranded on an alien planet was enough to teach even the great Rodney McKay some measure of control. "Well I didn't know _he_ had it in him until after we were married," he admitted.

Jeannie looked confused, "come again?" She asked.

"Aliens made us do it!" McKay said, slightly defensively. "We only got married because they had this silly tradition about people who step through the Stargate at the same time are meant to marry and we needed the ZPM we suspected was on their planet."

"Meredith, that's an awful reason to get married!" Jeannie chastised him.

"Oh and getting knocked up in college is better? At least by marrying John it saved lives in the end. We really needed that ZEP. Besides, it turned out okay in the end. More than okay." Rodney said with an expression of satisfaction and something that resembled peacefulness on his face. Jeannie was unfamiliar with this expression and she thought they suited him.

"So, when do I get to meet him?" She asked eagerly, ignoring the comment about her own marriage.

Rodney's face fell. "What? What is it, Mer?" Jeannie asked, full of sisterly concerned as she rested a hand on his arm in comfort.

"I…. I wish I could be stronger, for him. I'm always the one who panics and babbles uncontrollable and he's always there to yell 'McKay' at me and get me back on track so I can save the day or save the city or whatever… but now he's locked up and awaiting the IOA to sign off on his release and I can see it in his eyes that he doesn't think it's going to happen… I don't want to go back without him but I can't exactly say that without outing him!" Rodney explained, his voice pained and strained.

"Oh Mer, what have you got yourself into." Jeannie asked, holding him closely as they stood there, no words were exchanged just comfort from one member of family to the other.

TBC –

Okay people. There you have it. My okayish story that has been in my head for bloody years! More is coming soon but I am currently unhappy with chapter six and it requires rewriting, and since I'm busy this week with work and uni don't hold your breath! But I'm working on it! Thanks for your support.


	7. Chapter 6: Goodbye, Hello

**Chapter Six: Goodbye, Hello**

When Rodney returns to the base he is told that he has been cleared to return to Atlantis tomorrow morning. Elizabeth, they add, will not be going with him. Rodney argues and yells and calls them all the names under the sun that his enormous brain can come up with, but they don't budge. Due to the wraith threat (even though John, Elizabeth, and Rodney had all assured them that the Wraith were neutralized), they explain, they feel that a more military leader is needed. Someone with a background in fighting aliens, not a diplomat.

"What about John then?" Rodney asks. It's a reasonable question, Sheppard has all the necessary qualifications. He's military through and through despite his innate laziness and predilections for male scientists by the name of McKay. And no one has more experience fighting the Wraith than he does! No one.

But Rodney notes the near-unreadable exchange of glances and he knows he's already lost this battle. Pain sears though him and he almost doesn't neat the IOA representative as she explains that the Major's case is being looked at, but honestly he doesn't need to hear it, he already knows what they are going to say.

When he is dismissed he finds himself walking and ends up outside John's room; his cell. The guards give him knowing looks that make Rodney think maybe the room isn't as soundproof as John had promised, but right at that moment he couldn't care less. He enters unannounced and John springs off the bed at the site of him.

"They're sending me back tomorrow. Without you." Is the best Rodney can do because his voice is hoarse with emotion that he's too afraid to feel.

John's expression goes from pain to panic to fury before tightening up and becoming unreadable. "It'll be okay." He promises but Rodney knew if they were still kids then John would be saying that with fingers crossed behind his back because there is no way that either of them believe that lie.

"I love you," Rodney replies, the only truth he has to offer them both. John just swallows, nodding and trying to smile as they embrace. Their last night together is spent with shaky breaths and careful caresses. They never remove their clothes or even kiss, and in the morning Rodney feels like he's being sent to the gallows as he leaves John's room.

"Ready, McKay?" O'Neill asks him as he heads to the gate-room. He spares Jack a terse nod but otherwise avoids looking at anyone and speaking at all, which was so very unusual for him. If John – or even Elizabeth, Teyla, Ronan – were there they would be exchanging worried looks trying to find out what was wrong with him. God he missed them all. And the worst part was knowing that that feeling wouldn't be going away anytime soon.

"Sam?" He asked in surprise as he saw her in the gate room all packed up and ready to go with him, as well as Daniel Jackson and a about twenty anonymous marines. Supplies were already being sent through the gate.

"Rodney, they didn't tell you? I'll be Atlantis's new commander." She revealed.

Rodney just stares at her, feeling like someone had pulled the rug out from under his feet. If they were assigning Samantha Carter then there was a chance they were serious about not letting John go. Ever.

And there was nothing he could do about it.

So he nodded in her direction, and then turned away from her and Daniel as the two old friends chatted about how excited and nervous they were. Finally it was their turn to go through and Rodney couldn't help but feel like it was a betrayal of John and Elizabeth to be retuning with Sam and Daniel. He looked around at the people who he had lived with for the past ten years and hated that he could see his own disappointment and pain reflected in some of their eyes. Then Kelac approached him, and Rodney felt a whole new level of pain.

"Where is she?" He asked, his voice rough and tense.

"I'm so sorry." Rodney said, his eyes wide and watery.

"No. No, Rodney I didn't ask you if you were sorry. I asked you where Eliz is!" Kelac corrected him.

"With John," Rodney spat out, "back on Earth. They wouldn't let them return." He explained, oblivious to Sam and Daniel's watchful gazes.

Kelac's eyes went dull with pain. "Then I am sorry too, McKay. It seems we have both lost more than we ever hoped to have." He said and bowed formerly before backing away, the site of a defeated man.

"Was that-" Sam began, her tone shocked and surprised.

"Yes." Rodney bit out.

"I had no idea that-"

"Well it's too late now anyway, isn't it." Rodney snapped unfairly, choosing that moment to storm away to his quarters.

Sam shared a concerned look with Daniel before introducing herself and reciting the prepared speech that she hoped would ease the transition from Elizabeth's reign to Sam's leadership. It was going to be tough no matter what she said, but that didn't mean she shouldn't try to reassure them.

After her carefully chosen words had been spoken and assimilated by the suspicious and cautious expedition team, Sam introduced herself to Teyla Emmagen, a serene looking woman with coppery skin and hair only a shade or two darker.

"Teyla Emmagen, I presume." Sam said, projecting friendliness even though she felt like she was being examined. Teyla gave her a cool look although Sam felt no threat or hatred coming from the other woman.

"Colonel Carter. Welcome to Atlantis." Teyla greeted her, spreading her arms out in a gesture that encompassed the facility.

"I must say it's truly spectacular. I am honoured to be here." Sam said. "Truthfully when we didn't hear from Elizabeth or Sumner after the first transmission we assumed you had perished in the fight against the Wraith. Lets just say its very pleasing to discover Atlantis and the people have survived."

"Not just survived, but thrived. Atlantis is now completely self-sufficient with her own crops on the mainland that keep us in food, and many refugees on the mainland keep herds that provide both sustenance and clothes." Teyla said pointedly and Sam received the message loud and clear; Atlantis did not need Earth, and there had obviously been some resistance to re-establishing contact.

"Well that's good to know. This is my college, Dr Daniel Jackson. He'd like to talk to you if that's okay?" Sam said, still smiling politely.

Teyla turned to the man in surprise and bowed her head slightly. "Dr Jackson. Welcome. May I ask you, are you a doctor like Rodney or Carson?" She queried.

Sam hid a smile. "Uh, neither. You see on Earth 'doctor' can be used for a professional of many different areas. Psychology, medicine, science, anthropology… I'm an anthropologist and an archaeologist. Most of my work in the last seventeen years has been on the Stargate and the Ancients, in fact I even ascended once although I obviously have no memories of that time." Daniel explained in a rather long-winded way as he glanced around the control room looking at al the glory he had been denied when Jack hadn't allowed him to come with the expedition the first time around.

"I see," Teyla said with a polite smile.

"Daniel is interested in people and cultures. If you could show him around the city, give him access to some of the databases that the Ancients kept on their own society and Ascension, and perhaps share with him some of the ways of your own people?" Sam 'suggested', and Teyla nodded and led Daniel out of the control room. Then Sam finally let out a breath. What a journey this would turn out to be!


	8. Chapter 7: Missing

**Chapter Seven: Missing**

"So," Daniel began, "why don't you tell me a little about yourself. You're native of Pegasus right, but not of Atlantis?" He asked her.

"That is correct. The city was abandoned for quite some time before the expedition team arrived here ten years ago. I am Athosian, the first people that Colonel Sumner and Major Sheppard encountered, we explained to them about the Wraith and when my people were culled, Major Sheppard and Dr Weir offered us shelter on Lantea. Ever since we have been close allies." Teyla informed him.

"If you do not mind," she continued, "I wish to stop by my quarters first and then Rodney's. I have a surprise for him that I believe will brighten his mood considerably, although obviously I cannot hope to make up for the fact that Major Sheppard is not with us presently."

Daniel looked surprised at this, but nodded and followed her down a cool blue corridor, into a lift that he made a note of to ask her about that later. Another corridor and finally she stopped, waving a hand over a panel and the door to her quarters opened. Inside was a largish room with a bed and a sofa, plants and books spread around as well as two odd looking batons propped up in one corner. A dark haired man came into the room. "Teyla, what is the news?" He asked, his accent similar to Teyla's, as was his way of phrasing sentences.

"It is as Elizabeth feared. Both she and John are on Earth unable to return. Things are uncertain. For now we will have to live under Colonel Carter's command," Teyla informed him, sharing his look of sorrow and serene acceptance. "This is Dr Daniel Jackson, I am showing him the city. Dr Jackson, this is my husband Kanaan. Rodney has returned to us and I though Chitara and Liron would cheer him up," she said, and he nodded.

"They are in the den with Torren. I will get them." He disappeared and seconds later returned with three children following him. One was obviously a result of Kanaan and Teyla's union, but the other two were doubtfully related. Teyla's son – Torren – was about five years old however the other two were older, a girl about nine or so with flame red hair and inquisitive grey eyes, and the boy – roughly fourteen years old – who was lanky with skin pale as snowfall and sandy brown hair. Jackson felt very much the outside as he watched how the five of them interacted with one another.

"Is he home?" The girl asked excitedly as Teyla picked up her son.

"Rodney has returned, Chitara. However… I am sorry, especially to you Liron as I know how close you are to John. I am afraid he has been… detained. Do not fret though, not one of us is prepared to rest until he comes home. For now I thought it would be nice to see Rodney," she told them, not talking down to them but treating them as adults. The children nodded, accepting her words even though the boy (Liron) tensed and Chitara reached out instinctively and took a-hold of his hand, clutching it in her own.

"I want to see him," Chi said, a determined expression on her young face.

Teyla nodded, looking from one child to the other. "Liron, will you take her to Rodney's quarters? I must show Dr Jackson around," she asked and Liron nodded, his expression stony.

The children set off hand in hand, disappearing into a transporter. "Are they okay to roam the city on their own?" Daniel asked. It was strange for him too see children on the base, for to him it was like another SGC however he failed to appreciate the fact that Atlantis was a city; it was home.

"They will be fine, Dr, both Chi and Liron have spent many summers running around the city exploring under Rodney and John's supervision." She explained, kissing her son before exiting the apartment.

"Are there many children here?" Daniel asked, curious now.

Teyla took her time to consider the question. "A few. Most women who fall pregnant go to the mainland for much of their pregnancy. It is a calmer, simpler life their and a Doctor visits them often only bring them back to Atlantis for the birth and any medical procedures. Once born very few of the mother's choose to return to the City fearing it will be invaded and their child will be at risk, or that the child will stumble across one of the Ancient labs and become ill. It has happened before. Consequently most children are raised on the mainland in a group environment, everybody looking out for each other, until they are old enough to be schooled and then they are taught agriculture and cooking, sowing and hunting by my people, and maths and science by the Atlantis residence. Liron and Chitara spend much of their time on the mainland however their guardians are John and Rodney respectively."

"I never imagined Rodney the father type! I wonder how that happened." Daniel said lightly. This place – these people – were nothing like he had believed.

Teyla gave him an unreadable look. "The story is not for the faint hearted," she assured him. "Come, this is the way to one of the labs," she changed the subject and steered him to the left.

A knock woke Rodney from his self-pity. He sighed, fearing it was Sam come to bug him about one of the systems or Carson here to question him about everything that had happened on Earth. He would have ignored it but whoever it was they were persistent and Rodney finally gave in. "What is I-" He stopped, looking into the cautious eyes of his adopted daughter Chitara.

"You're back!" Liron sounded almost accusing and Rodney could only guess at how he must have been feeling. Both Liron and Chitara were orphans of the Pegasus Galaxy, saved and cared for by John and himself much like Cassandra had been adopted by Dr Janet Frazier back on Earth. Hopefully this story would have a happier outcome than Janet and Cassandra's.

"I am," he agreed. "But John had to stay on Earth for a few more.. for a little while longer," he added lamely wishing he had more to give the boy who looked like he was about to kill something with his flinty eyes and clenched fists. Truth was Liron was just a broken kid and John had been fixing him. Without John, Liron was still broken.

"I missed you!" Chitara cried, launching herself into Rodney's arms. First time she had done that Rodney had near had a heart attack, he'd never exactly spent much time with children and even as a child hugs had been rare in his house. He was better now, he could even bend down to embrace her properly and whisper in her ear the he too had missed her. He had missed them both, and now they were all missing John.

He guided them inside and set up a DVD, listening as Chi babbled over the Doctor Who episode about all the things she had learnt while he was gone, from some new words that one of the Athosians had taught her to a skipping game she now played with the other children. Liron remained quiet and observed both his 'sister' and Rodney while he pretended to watch the film. Eventually both children wore themselves out and fell asleep on the bed Rodney and John had once – and would again if he had anything to say about it! – shared. With his resolve solidified by the ache he had seen on Liron's face and the dismay on Chi's, he left the room, ordering it to lock against anyone entering but to allow Liron and Chi to leave if they wished, and headed off to Sam's new shiny office.

"Rodney," she greeted him warmly, looking a bit frazzled as she went through some of the reports and mission proposals.

Rodney looked uncomfortable as he entered, wishing that Elizabeth was seated behind that desk and not his once-fantasy Samantha Carter. "I wanted to know if you were told how long your commission here would last?" He asked her, meeting her eyes with a courage he did not feel as his stomach churned with nausea.

Sam looked down, away from him as she gathered her thoughts, and back up at him. "I was told that pending a year review I should expect this post to be indefinite. I'm sorry, Rodney," she added, obviously understanding that he wanted Elizabeth back.

"Can't you let them back? Elizabeth has a husband, John has family too. Even if Elizabeth isn't expedition leader anymore can't you just try?" Rodney begged.

Sam's eyes widened. "I… uh… I can certainly try but that doesn't mean I will succeed. She would be useful, perhaps make a team dedicated to brokering deals and put her in charge of negotiations… I can ask but John… he's out of my control. No matter what happens it will be up to the IOA and the Generals if he comes back or not."

Rodney pursed his lips. "We need him. More than you realise. Atlantis needs him."

Sam nodded. "I understand, Rodney. I wish I could do more. I'll recommend that both Weir and Sheppard are assigned back here in whatever capacity but I can't make promises. You said he had family here? Does he have a wife?" She asked.

Rodney barely managed not to flinch. "A son," he ground out. "An adopted son who needs him very much."

"I'll see that it gets noted. Thank you for telling me this, Rodney," she added, sounding genuine.

He turned to leave, pausing at the threshold, "I… Good luck with your new command, Sam," he tod her before leaving.

=== THANKS SO MUCH TO THOSE WHO HAVE COMMENTED IT MEANS A LOT!!!!!

TBC


	9. Chapter 8: A Word of Warning

**Chapter Eight: A Word of Warning **

I had been a whole week. An agonising, long, painful week full of sleepless nights where he missed he warmth of John's body next to his own, and his day's were lonely and stressful without John's spontaneous appearances to cheer him up. Everybody noticed, but no one dared say anything. After all Rodney's loss was everyone's loss.

Sam was fitting in well considering. Not that that was a surprise since she was Samantha Carter! Rodney knew it wasn't the city betraying Elizabeth, everybody missed her, but it was Kelac who was struggling. He had returned to his planet of birth to spend time teaching while he awaited for Rodney to make sure his beautiful 'Eliz' came back home. Daniel still hadn't left, he was fascinated by everything Ancient, from the architecture, their history, the native food and animals and most especially how they ascended. When Rodney joked that it would take his entire lifetime to learn even ten percent of what he wanted to, Daniel took him seriously and started negotiations with Landry and Carter to move to Pegasus permanently. It didn't seem fair that Daniel – a stranger to the city – could come and go as he pleased whereas Elizabeth and John, who had kept the city going in the absence of power and regulations, when the enemy had been literally at there door, and they were being punished for actions others second guess when they have the benefit of foresights and none of the experience of combat.

It was a week too long, Rodney decided. He had been to kind of Sam, giving her more credit, assuming she had more sway with the SGC than she apparently had. She was after all their poster girl for sexual equality, brains and beauty. There was nothing Colonel/Dr Samantha Carter couldn't do, it seemed, except for bring back John. Finally she was so irritated after three whole days of being almost constantly pestered with emails from Rodney, that she gave him this advice, "if you're so determined to use every single insult in your wide vocabulary then why don't you aim them at someone more appropriate?". And that was exactly what he did.

Outgoing Address:

Stargate Command

Cheyenne Mountain

Colorado Springs

United States of America

Earth

The Milky Way

Return Address:

Dr M. R. McKay

Corridor XX58,

Central Building

Atlantis, Lantea

The Pegasus Galaxy

To Whom It May Concern:

Which, if you hadn't noticed just how brilliant and vital I am, is everyone in at least two galaxies.

I demand that you release Major John Sheppard of the United States Air Force, immediately. He is both necessary and vital to this mission, almost as vital as I am (since he has the strongest known incarnation of the ATA gene).

I am well aware of the reasons he has been detained, that the IOA deem it essential to second guess actions he made in the middle of a combat situation. If they require it, I am sure I could find one of the few remaining (albeit dying of starvation) Wraith and set up the situation in almost the exact same way which Major Sheppard experienced it, and let them make their own minds up whether or not to let an already dead man end his life at the hand of the enemy, or by the mercifully quick bullet of a comrades gun. There is only one answer they would give, I am sure of it.

Further more I demand that Major Sheppard be returned to Atlantis where he would be of the most use. The people trust him in a way that Colonel Carter (no disrespect meant, Sam) cannot hope to gain for years to come. By refusing to allow the return of the two leaders of this expedition, you have crippled Colonel Samantha Carter's own ability to build a relationship of trust with the people under her command.

My third demand is that Dr Elizabeth Weir be reunited with her husband. Surely good Christians like yourselves cannot think it is right to thwart God by ignoring a union he himself has blessed, (or whatever it is you people believe). Kelac misses her, and I'm afraid he may hurt me if I don't manage to success in fulfilling my promise to return Elizabeth to his side.

To summarise, we need our people back. Now.

In case you are thinking of ignoring this letter, I would think again. I am after all the most intelligent man in two galaxies and while I am sure given sufficient time and experience that Carter could manage not to kill us all and run the Science department, that wouldn't be possible as she is in a command position and cannot afford to split her focus. So really, I am your only hope. All this boils down to; I will quit if you don't return Major John Sheppard and Dr Elizabeth Weir to where they belong (here). If you refuse to let me through the Stargate, I am sure I can find a home for myself on one of the more advanced planets in the Pegasus Galaxy. Good luck finding out which one.

Yours, sincerely:

Dr M. R. McKay

Sam proof read it. Her mouth was on the floor before she had even gotten to the second paragraph and Rodney just thought it was a shame that he didn't have a camera to capture her speechlessness.

"You can't send this, Rodney!" She said, her eyes wide and shocked, hiding amusement and awe at how dedicated he was to getting Sheppard back. To threaten not only to quit his beloved Atlantis, but also to find refuge on a planet that was considerably less technologically advanced than even Earth was, was a huge thing for him to do. Sam obviously didn't have all the pieces of the puzzle, but one day she hoped to figure out why Rodney was so damned dedicated to John Sheppard.

"I can," he claimed arrogantly, "and I'm going to."

"I…. Fine. But I'm not counter-signing this. I value my career. And my life," she told him and handed him back the letter.

He nodded, he had expected nothing less. Jack O'Neill, now there was a man who had liked to stir things up. Sam, not so much. It was all part of her gold girl charisma. "That's fine. I just need you to give the nod to dial Earth and then we can get this over with."

Truthfully he was petrified that they would allow him to quit and prevent his return to Earth. He would have to go to one of the less civilised planets with Chitara and Liron, hoping that they never found him. They were after all a military operation and as such had no scruples when it came to falsely imprisoning people they considered useful, which was why he would technically be on the run. But that was worst case scenario. Well, worst case scenario would be they killed him, but it was a pretty close second. Besides, he was pretty sure Sam liked him enough to at least give him some warning if the plan was to gun him down over-dramatically in the gate-room. He hoped.

"Now all we can do is wait," Sam said as Rodney poked the letter through the event horizon.

__**__

It was a tense three days until the SGC finally contacted them. Landry's aging face appeared on the screen, and Rodney hovered in the background, getting ready to run for it if Sam gave him the nod.

"Colonel Carter, it's good to see you alive. We thought maybe Dr McKay would have staged a coup by now," Landry joked dryly, at least Rodney assumed that was what passed for humour with Generals.

Sam speared him a smile. "General, it's good to see you too. I assume this means that you have reviewed Dr McKay's request?" She asked. Everyone who was there, Kelac, Rodney, Radek, Carson, some of the Marines who had been close to John, and all of the Air Force personnel who had been with the expedition since the beginning. It was a bit crowded in the room, actually, Rodney found himself constantly trying not to elbow people, after all they had guns. Teyla was absent, but only because she was taking care of the three children. Liron had begged to be here, but Rodney had decreed it too stressful for young minds. Besides, he knew if it was bad news he would need a quick escape and to find somewhere safe to break down for an hour or so before leaving Atlantis forever.

_Oh god, please, please, please let my John come home_, Rodney begged silently.

"Indeed I have, if you could cal it that. A few of the IOA members wanted to call it a terrorists list of demands and said we shouldn't even bother to respond. Luckily for them, however, I convinced them we need him. Don't make me regret this McKay!" The General finished on a low warning note.

"You mean he's coming home!" Rodney wanted clarification before he let himself believe that this nightmare was almost over.

Landry narrowed his cold eyes in Rodney's general direction. "It means, Dr McKay, that after much discussion and evaluation, Major Sheppard has resigned his commission. Due to the strength of his gene, there was never any doubt that he would in some capacity remain with the SGC. After your letter, it was decided that Mr Sheppard would be allowed to return to Atlantis as a civilian contractor. There will be a few changes, especially to the military structure of the base, but otherwise his duties will remain the same; heading Atlantis Recon 1, flying Puddlejumpers, and using his gene in the activation and use of the Chair. He'll just have less paperwork." The General sounded almost envious.

"What about Dr Weir?" Sam asked, and Rodney could have kissed her because he was so happy John was returning that he had forgotten about Elizabeth's absence. He was sure that, given enough time, he would have remembered.

"Dr Weir will be remaining on Earth. However special permission has been given to her husband, Kelac? He is allowed to, should he chose, come to Earth to reunite with her. I believe that would satisfy the terms of your demands, Dr McKay?" He said dryly, and Rodney thanked all kinds of deities (that he didn't believe in) that he wasn't military or he believed he would be being reamed out right now.

"Sure," he agreed in a small voice.

John was coming home, John was coming home! The thought was repeating in his head, bring a smile to his lips.

"So, no more demands, Dr McKay or you may find yourself out of a job and living off Tava beans for the rest of your days. Now, I believed you wanted someone?" Landry said, and Rodney's gaze was drawn to the commotion in the gate room. People were congregating in the centre, hugging and yelling in joy. The crowd parted, and in the middle was a haggard looking John Sheppard dressed in a civilian uniform, a wide smile stretched across his face and a large duffle bag on the floor next to him. It was the best thing Rodney had ever seen.

"Rodney," John smiled at him.

"John," Rodney breathed. He wanted to hug him, to kiss him and hold him tight so that everyone knew he was Rodney's. For Rodney to know this was really John, and that everything was going to be okay now.

John grinned his bed-room-smile and Rodney frowned, forgetting in the excitement that John was a civilian now. "Come here," he said quietly.

Rodney glanced around. While yes, everyone knew they were married and most people did assume they were at it like bunnies, they had never confirmed this and many of the military men preferred to pretend it didn't mean anything. "Come here," John said insistently.

Rodney stepped forward, meeting John's insistent lips with a kiss so passionate that people were blushing when they parted. "I missed you," John said, breathing into Rodney's neck, memorising the scent of his lover, of his husband.

"I know. I love you," Rodney replied, happy to be in the arms of the man he would have given everything up for.

"I'd guessed," John admitted cheekily.

Rodney took his husband's hand and led him away, up the stairs and towards their quarters. He didn't hear Sam telling Daniel that suddenly everything made sense, but if he had all he would have done was smiled because as far as he was concerned, now that John was back where he belonged, everything did make sense.

FINISHED

AN// This concludes this plot. However I may, from time to time, write short sequels or prequels regarding Rodney and John, and maybe Kelac and Elizabeth. Maybe.

Thanks so much for reading. I hope you enjoyed this. I apologise for the bad spelling and grammar, I have a beta ready for my next story (Innate) but this is all me. Sorry!

Please feel free to leave a comment.


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